PDBsum entry 5f8h

Transferase/RNA

PDB id: 5f8h

Contents

Protein chain

462 a.a.

DNA/RNA

Ligands

SO4

Metals

_MG

_ZN

Waters ×141

PDB id:

5f8h

Name:

Transferase/RNA

Title:

Enterovirus 71 polymerase elongation complex (c1s1/2 form)

Structure:

Genome polyprotein. Chain: a. Fragment: unp residues 1732-2193. Engineered: yes. RNA (35-mer). Chain: b. Engineered: yes. RNA (5'-r( Up Gp Up Up Cp Gp Ap Cp Gp Ap Gp Ap Gp Ap Gp A)- 3').

Source:

Enterovirus a71. Organism_taxid: 39054. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Organism_taxid: 32630

Resolution:

2.45Å R-factor: 0.200 R-free: 0.244

Authors:

B.Shu,P.Gong

Key ref:

B.Shu and P.Gong (2016). Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation. Proc Natl Acad Sci U S A, 113, E4005. PubMed id: 27339134 DOI: 10.1073/pnas.1602591113

Date:

09-Dec-15 Release date: 22-Jun-16

Protein chain

E5RPG2  (E5RPG2_HE71) -  Genome polyprotein from Human enterovirus 71

Seq: 2193 a.a.

Struc: 462 a.a.

DNA/RNA chains

G-G-U-C-U-C-U-C-U-C-G-U 12 bases

A-C-G-A-G-A-G-A-G-A 10 bases

Enzyme reactions

• Enzyme class 2: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 3: E.C.3.4.22.28 - picornain 3C.
• Reaction: Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
• Enzyme class 4: E.C.3.4.22.29 - picornain 2A.
• Reaction: Selective cleavage of Tyr-|-Gly bond in the picornavirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
• Enzyme class 5: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.1602591113

Proc Natl Acad Sci U S A 113:E4005 (2016)

PubMed id: 27339134

Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation.

B.Shu, P.Gong.

ABSTRACT

Viral RNA-dependent RNA polymerases (RdRPs) play essential roles in viral genome replication and transcription. We previously reported several structural states of the poliovirus RdRP nucleotide addition cycle (NAC) that revealed a unique palm domain-based active site closure mechanism and proposed a six-state NAC model including a hypothetical state representing translocation intermediates. Using the RdRP from another human enterovirus, enterovirus 71, here we report seven RdRP elongation complex structures derived from a crystal lattice that allows three NAC events. These structures suggested a key order of events in initial NTP binding and NTP-induced active site closure and revealed a bona fide translocation intermediate featuring asymmetric movement of the template-product duplex. Our work provides essential missing links in understanding NTP recognition and translocation mechanisms in viral RdRPs and emphasizes the uniqueness of the viral RdRPs compared with other processive polymerases.